feat: docker image for SandboxAQ/aqaffinity

[jandom]

Summary

Here is the experimental build I did on an AWS g5.xlarge with the deep learning AMI as base image.

Requires to be logged into hugging face cli locally, to clone the repo at image build. Confirm login with

hf auth whoami
user:  my-username
orgs:  my-orgs

Build with

docker build \
    -f docker/Dockerfile \
    --secret id=hf_token,src=$HOME/.cache/huggingface/token \
    --target affinity \
    -t openfold-docker:affinity .

Run with

docker run --rm \
    --gpus all \
    --ipc=host \
	-v "${HOME}/.openfold3/:/root/.openfold3" \
	-v "/home/ubuntu/workspace/openfold-3:/opt/openfold3" \
    -v "${PWD}/output:/output" \
    -it openfold-docker:affinity \
    aqaffinity predict \
        --query_json ./examples/example_inference_inputs/query_single_protein_single_ligand.json \
        --runner_yaml ./examples/example_runner_yamls/affinity.yaml \
        --num_diffusion_samples=1 \
        --use_templates=false \
        --output_dir /output \
        --binding_affinity_ckpt_path /opt/aqaffinity/model_weights/model_weights_only.pt

And then the output will be in

cat output/mcl1/seed_42/mcl1_seed_42_sample_1_binding_head.txt 
-2.8919382095336914

Changes

• new target 'affinity' in the Dockerfile, very easy to incorporate the SandboxAQ package

Related Issues

Testing

Other Notes

[jnwei]

LGTM, but maybe this would be a PR better suited for the Sandbox AQ affinity repo itself?

Two small comments:

• Could you mention the system that you tested this docker image on?
• I have a suggestion regarding the example file naming, see in comment in line.

[jnwei]

Can we reuse any of the existing examples?

The current file name query_single_protein_ligand_affinity.json suggests to me that there is a difference between the inputs required for affinity prediction vs the inputs for openfold3 inference. From a glance, it doesn't look like there are any additional input fields required for the affinity modle.

If we want a simpler protein/ ligand filename, perhaps we could name the example file query_single_protein_single_ligand.json?

[jandom]

Correct, and i was surprised by that too – it only works on single-chain, single-ligand complexes. None of the examples, as far as I could see, had that.

We should probably document that behavior somewhere.

+1 to simpler filename, yeah

[jandom]

Updated the filename now

[jandom]

Could you mention the system that you tested this docker image on?

Thanks for the review, really good as always 🙌 Updated the PR description above (it was g5.xlarge)